With a respected expert now overseeing a detailed food-safety strategy, the Mexican restaurant chain Chipotle is determined to win customers back and rebuild its battered reputation.

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A large digital kitchen timer perches near a sink at a Chipotle Mexican Grill in the Meatpacking District of Manhattan. It is reset every 30 minutes, and 12 minutes have passed.

“In about 18 minutes, everyone will stop what they’re doing and wash their hands,” said James Marsden, the company’s new executive director of food safety.

There isn’t much sexy about food safety, and that goes for regular reminders to scrub hands. But for the last year, Chipotle has been forced to focus on little else, after a string of illnesses among diners at the Mexican restaurant chain grew into nationwide alarm. The concern has battered Chipotle’s sales, reputation and stock.

Kitchen timers occupy a similar position in each of Chipotle’s more than 2,000 restaurants, a symbol of the company’s efforts to prevent similar problems in the future. On Wednesday, Chipotle highlighted several new initiatives as well, including work it is doing to enhance food safety among its suppliers, hoping that pointing to the moves will help regain the public’s confidence — and profits.

At the center of the action is Marsden, a longtime academic whom Chipotle hired in the spring.

In one of his first extended interviews since arriving, he said his challenge had been clear: to allow Chipotle to continue using fresh ingredients — not frozen or precooked — while making its farm suppliers, food and restaurants safer.

“Anybody can spray a bunch of chemicals around and improve food safety,” he said. “This was going to require something more innovative and different.”

Big challenge

Marsden and the company have their work cut out for them. First, they will need to convince Americans that the company’s food is safe. Then, they need to get those people back into the restaurants.

For many months now, the company has offered an array of promotions, most recently free drinks for high school and college students who buy a meal.

“I’m not sure it’s accomplishing what they want,” said Mark Kalinowski, an analyst at Nomura Securities. “When you’re giving away food, it’s discounting — and to me, this isn’t a brand built on discounting so it creates some new questions about the future.”

Some sales have returned, but more slowly than investors expected, and shares have fallen 45 percent in the last year. Even Steve Ells, the company’s founder and co-chief executive, said he thought the company would rebound faster.

Yet Ells also noted that Chipotle was in “uncharted waters.”

“No one has ever had this kind of a food-safety crisis in the era of social media,” Ells said.

Jack In The Box — a burger chain where more than 700 people got sick in 1993 after eating E. coli-contaminated meat — “never had to deal with Facebook and Twitter,” he said.

Chipotle’s problems began in August 2015, when more than 200 people were sickened with norovirus after eating at one of its restaurants in Simi Valley, Calif. The same month, 64 people who ate at one of 22 Chipotle restaurants in Minnesota and Wisconsin got salmonella poisoning.

But it wasn’t until November, when the company announced it had closed a string of stores across the Pacific Northwest because of E. coli contamination, that investors began to flee.

The next month, there was another E. coli problem in the Midwest. And in February, some 200 people got sick with norovirus after eating at a Chipotle in Boston.

“Part of the thing that was so devastating was because there were multiple incidents, and so it may have looked like we were out of control,” Ells said.

“We had good food-safety standards in place, but were they good enough to ensure something like this wouldn’t happen given the momentum of our business and that we rely on fresh ingredients prepared on the spot? Maybe not.”

Chipotle began looking around for a food-safety expert to hire. The company found Marsden, a soft-spoken man who had recently retired from teaching at Kansas State University. (He is also the father of the actor James Marsden, best known as Cyclops in the “X Men” film series.)

Marsden had a long history of dealing with food-safety crises, including a stint at the American Meat Institute during the Jack In The Box crisis. The Chipotle situation intrigued him. “This was an interesting case involving multiple pathogens and multiple outbreaks, but with no precise indication of the cause,” he said.

Covering the bases

So Marsden put together a plan to cover practically every base — from ensuring employees are checked every morning for illnesses to frequently checking the temperature of foods — all of which must be logged into “the black book,” a daily record of each location’s safety procedures.

Some of those procedures are something of a throwback to old-school food-safety practices.

Guacamole, for instance, now takes advantages of the cleansing properties of the lemon and lime juices in the recipe. Before getting mixed, the chopped tomatoes, onions and jalapeños are laid on top of avocados and drizzled with citrus juices in one last effort to ensure food safety.

Some scientists may question such tactics, saying they have been supplanted by newer methods. But Marsden said he was confident in them.

“We’re doing research and are going to publish papers on what we’re doing, so people can see for themselves that it works,” he said.

Lettuce is now rinsed, drained and immersed in a solution of vinegar and water and drained again. It then is chopped, immersed in an antibacterial solution and rinsed again. And if any sediment is left in the sink, the chopped lettuce is washed in the solution again.

In addition, two employees must verify that produce like onions, jalapeños and avocados have been immersed in hot water for five seconds to kill germs on their peels. Containers storing the food must get a printed sticker indicating when they were sanitized and when they should be discarded if not used.

Chicken is now marinated in the evening, when restaurants are less busy, to reduce risk of cross contamination, instead of whenever there is time.

And all of this is overseen by a food-safety leader in each restaurant, a new position.

The leader must also ask every employee how they feel before they clock in, to make sure they aren’t coming to work sick, and keep records when an employee is sent home because of illness.

Robert Gravani, who teaches food safety at Cornell University, said what he had heard about what Chipotle was doing under Marsden’s direction seemed good.

The trick, he said, will be training employees to stick with the new programs.